Multiple sequence alignment - TraesCS5D01G337500

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS5D01G337500 chr5D 100.000 2444 0 0 1 2444 426284689 426282246 0.000000e+00 4514
1 TraesCS5D01G337500 chr5D 100.000 247 0 0 2777 3023 426281913 426281667 9.880000e-125 457
2 TraesCS5D01G337500 chr5D 96.667 90 3 0 1377 1466 426283226 426283137 1.880000e-32 150
3 TraesCS5D01G337500 chr5D 96.667 90 3 0 1464 1553 426283313 426283224 1.880000e-32 150
4 TraesCS5D01G337500 chr5A 95.827 2444 95 5 1 2444 540381953 540379517 0.000000e+00 3941
5 TraesCS5D01G337500 chr5A 95.492 244 8 1 2780 3023 540379414 540379174 1.310000e-103 387
6 TraesCS5D01G337500 chr5A 96.667 90 3 0 1464 1553 540380579 540380490 1.880000e-32 150
7 TraesCS5D01G337500 chr5A 95.556 90 3 1 1377 1466 540380492 540380404 3.140000e-30 143
8 TraesCS5D01G337500 chr5B 95.046 1756 71 4 689 2444 516063068 516061329 0.000000e+00 2747
9 TraesCS5D01G337500 chr5B 97.976 247 5 0 2777 3023 516060963 516060717 2.150000e-116 429
10 TraesCS5D01G337500 chr5B 89.097 321 24 5 1 315 516063383 516063068 3.650000e-104 388
11 TraesCS5D01G337500 chr5B 97.778 90 2 0 1377 1466 516062293 516062204 4.040000e-34 156
12 TraesCS5D01G337500 chr5B 96.667 90 3 0 1464 1553 516062380 516062291 1.880000e-32 150


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS5D01G337500 chr5D 426281667 426284689 3022 True 1317.75 4514 98.3335 1 3023 4 chr5D.!!$R1 3022
1 TraesCS5D01G337500 chr5A 540379174 540381953 2779 True 1155.25 3941 95.8855 1 3023 4 chr5A.!!$R1 3022
2 TraesCS5D01G337500 chr5B 516060717 516063383 2666 True 774.00 2747 95.3128 1 3023 5 chr5B.!!$R1 3022

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
477 484 0.244994 AGCTGGTGTCTCTAAGCACG 59.755 55.0 0.0 0.0 38.14 5.34 F
502 509 0.323360 GGCACCTCCAATGGCAGTAA 60.323 55.0 0.0 0.0 42.03 2.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1582 1589 0.392193 AGATTTGTGAGCCGCTGGAG 60.392 55.0 0.0 0.0 0.0 3.86 R
2364 2371 0.460987 CCTGATCAAGCTCCGTCACC 60.461 60.0 0.0 0.0 0.0 4.02 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
90 97 1.134818 CGATTCCGTGGTGAATGGAGA 60.135 52.381 0.00 0.00 45.05 3.71
477 484 0.244994 AGCTGGTGTCTCTAAGCACG 59.755 55.000 0.00 0.00 38.14 5.34
502 509 0.323360 GGCACCTCCAATGGCAGTAA 60.323 55.000 0.00 0.00 42.03 2.24
517 524 2.202878 TAACAGCGCCGATGCCTC 60.203 61.111 0.56 0.00 34.65 4.70
569 576 2.116983 GACCAGGCAGCAGGACAAGA 62.117 60.000 9.95 0.00 0.00 3.02
667 674 1.303236 CCTCGGGCAAATGTCCACA 60.303 57.895 4.73 0.00 40.62 4.17
683 690 1.985662 ACAATCCGGTCGGCCTACA 60.986 57.895 9.95 0.00 34.68 2.74
759 766 0.904649 ATCACCTTGAGTGCATCGGA 59.095 50.000 0.00 0.00 46.81 4.55
779 786 4.201792 CGGAAAGCTTCTTCACATGAGATG 60.202 45.833 0.00 0.00 0.00 2.90
810 817 6.291377 TCTAAGAGGATGTGATGGCATTTAC 58.709 40.000 0.00 5.15 0.00 2.01
863 870 6.451393 GGCAACTCGAAACTCTAGATATCAT 58.549 40.000 5.32 0.00 0.00 2.45
898 905 1.866483 AAGGCTGCCATGGACCATCA 61.866 55.000 22.65 1.84 0.00 3.07
908 915 4.209538 CCATGGACCATCATCAAGCTTAA 58.790 43.478 5.56 0.00 0.00 1.85
947 954 1.699634 TGCTGGGGCCATAGAAGATAC 59.300 52.381 4.39 0.00 37.74 2.24
1098 1105 6.953520 TGAAAAAGAAGATGGGTATGGATGTT 59.046 34.615 0.00 0.00 0.00 2.71
1258 1265 1.530419 ATCACACGGGCAAAAGCCA 60.530 52.632 8.94 0.00 0.00 4.75
1320 1327 4.207891 AGGAGTGATTAGCGTCAACAAT 57.792 40.909 0.00 0.00 0.00 2.71
1323 1330 4.508124 GGAGTGATTAGCGTCAACAATAGG 59.492 45.833 0.00 0.00 0.00 2.57
1339 1346 5.564550 ACAATAGGAGCAGTCAAGATTTGT 58.435 37.500 0.00 0.00 0.00 2.83
1343 1350 5.859205 AGGAGCAGTCAAGATTTGTTTTT 57.141 34.783 0.00 0.00 0.00 1.94
1412 1419 6.497259 TCACTGGGATATCCTGGTTTATCTAC 59.503 42.308 21.18 0.78 38.62 2.59
1522 1529 2.773661 TGCTTAGATGGCATCTCCTCAA 59.226 45.455 31.94 19.55 40.76 3.02
1572 1579 6.072397 AGCTGTACGGCAACATTGTAAAATTA 60.072 34.615 27.85 0.00 34.17 1.40
1576 1583 4.281182 ACGGCAACATTGTAAAATTACCCA 59.719 37.500 1.13 0.00 32.72 4.51
1582 1589 7.525759 CAACATTGTAAAATTACCCAAATGGC 58.474 34.615 14.31 0.00 37.83 4.40
1588 1595 1.780503 ATTACCCAAATGGCTCCAGC 58.219 50.000 0.00 0.00 37.83 4.85
1673 1680 5.069251 CCATACAACTCCTTCCGAAGATACT 59.931 44.000 9.87 0.00 0.00 2.12
1680 1687 6.366340 ACTCCTTCCGAAGATACTGAATCTA 58.634 40.000 9.87 0.00 44.56 1.98
1754 1761 2.107204 ACTTCTGTCAAGGTGCATTCCT 59.893 45.455 0.00 0.00 39.84 3.36
1820 1827 7.410120 AATTGGTGAAGTTTGAAGAAGAAGT 57.590 32.000 0.00 0.00 0.00 3.01
1853 1860 2.428071 GCTGCTGCAGTTTCGTGC 60.428 61.111 28.50 11.47 44.27 5.34
1955 1962 2.093869 TCCACAACGGCTACAAGGATAC 60.094 50.000 0.00 0.00 33.14 2.24
2000 2007 3.841643 AGCTGGCAAAGAATCAAAATCG 58.158 40.909 0.00 0.00 0.00 3.34
2203 2210 5.941948 AAGGCATTGTAACACAGAACTAC 57.058 39.130 0.00 0.00 0.00 2.73
2212 2219 8.902540 TTGTAACACAGAACTACAAATCATCT 57.097 30.769 0.00 0.00 33.69 2.90
2364 2371 0.541863 ATTTAGGCAGGGGTGAGTCG 59.458 55.000 0.00 0.00 0.00 4.18
2368 2375 3.311110 GCAGGGGTGAGTCGGTGA 61.311 66.667 0.00 0.00 0.00 4.02
2871 2911 2.545526 TCGCTTAATGCAGCAATAGAGC 59.454 45.455 0.00 6.27 43.06 4.09
2876 2916 1.964552 ATGCAGCAATAGAGCCTGTC 58.035 50.000 0.00 0.00 34.23 3.51
3018 3058 9.681062 TTTGAAATGGAGGAGTACTAAAATAGG 57.319 33.333 0.00 0.00 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
71 77 2.555199 CTCTCCATTCACCACGGAATC 58.445 52.381 0.00 0.00 35.37 2.52
301 308 2.432628 GACTGACCGCCAAGTCCG 60.433 66.667 0.00 0.00 35.83 4.79
372 379 3.879682 CATCCGCATGGCCACACG 61.880 66.667 19.70 19.70 34.14 4.49
517 524 2.256174 CTTCATTGATGCCAAACAGCG 58.744 47.619 0.00 0.00 37.55 5.18
569 576 1.296715 GGGCGAGATCCACACTTGT 59.703 57.895 0.00 0.00 0.00 3.16
609 616 3.379688 CACCGAGATCACTCTGAGATCAA 59.620 47.826 12.44 0.00 43.35 2.57
660 667 2.660206 CCGACCGGATTGTGGACA 59.340 61.111 9.46 0.00 37.50 4.02
667 674 0.325602 TTTTGTAGGCCGACCGGATT 59.674 50.000 9.46 1.62 42.76 3.01
683 690 6.953101 AGTTCACCTTTACATTTGGGTTTTT 58.047 32.000 0.00 0.00 0.00 1.94
726 733 4.935205 TCAAGGTGATGGTCAACTAATTCG 59.065 41.667 0.00 0.00 45.11 3.34
759 766 3.442977 GGCATCTCATGTGAAGAAGCTTT 59.557 43.478 0.00 0.00 0.00 3.51
810 817 1.308069 CCAACGAATCTGGCAGGTGG 61.308 60.000 15.73 3.73 34.91 4.61
863 870 2.436542 AGCCTTATTATGCGTGTACCCA 59.563 45.455 0.00 0.00 0.00 4.51
908 915 4.094887 CAGCACAAATGTTCCGTAGCTTAT 59.905 41.667 0.00 0.00 0.00 1.73
947 954 4.872124 TGATTTCAAGTCTGTCATCATCGG 59.128 41.667 0.00 0.00 0.00 4.18
973 980 5.302059 CCTCGGGTAGATCTTCTTGACATTA 59.698 44.000 0.00 0.00 0.00 1.90
974 981 4.100189 CCTCGGGTAGATCTTCTTGACATT 59.900 45.833 0.00 0.00 0.00 2.71
1098 1105 1.590525 GTCACGCCTGTTCACGTCA 60.591 57.895 0.00 0.00 41.32 4.35
1171 1178 2.715005 CACTGCAACACCACGTGG 59.285 61.111 32.83 32.83 37.94 4.94
1258 1265 5.356291 AGCTCTTCTATGTCTTGCAGAAT 57.644 39.130 0.00 0.00 0.00 2.40
1309 1316 1.276421 ACTGCTCCTATTGTTGACGCT 59.724 47.619 0.00 0.00 0.00 5.07
1320 1327 6.239008 CCAAAAACAAATCTTGACTGCTCCTA 60.239 38.462 0.00 0.00 0.00 2.94
1323 1330 4.209911 GCCAAAAACAAATCTTGACTGCTC 59.790 41.667 0.00 0.00 0.00 4.26
1339 1346 2.433604 TGAGACCTGCAATTGCCAAAAA 59.566 40.909 26.94 7.59 41.18 1.94
1343 1350 1.246056 GCTGAGACCTGCAATTGCCA 61.246 55.000 26.94 15.14 41.18 4.92
1412 1419 1.698532 AGGAGATGCCATCTAAGCAGG 59.301 52.381 7.30 0.00 44.90 4.85
1522 1529 2.560105 GGCTTTGAAGATTTGCTGGAGT 59.440 45.455 0.00 0.00 0.00 3.85
1576 1583 2.439156 GAGCCGCTGGAGCCATTT 60.439 61.111 0.00 0.00 37.91 2.32
1582 1589 0.392193 AGATTTGTGAGCCGCTGGAG 60.392 55.000 0.00 0.00 0.00 3.86
1588 1595 1.391485 CTTGACGAGATTTGTGAGCCG 59.609 52.381 0.00 0.00 0.00 5.52
1619 1626 2.016096 GCTCCACAATCCTTGAGCTCC 61.016 57.143 12.15 0.00 45.21 4.70
1652 1659 5.258841 TCAGTATCTTCGGAAGGAGTTGTA 58.741 41.667 17.19 0.00 38.15 2.41
1673 1680 3.254411 CAGGCGCAGAGTAGATAGATTCA 59.746 47.826 10.83 0.00 0.00 2.57
1680 1687 0.684479 TCCACAGGCGCAGAGTAGAT 60.684 55.000 10.83 0.00 0.00 1.98
1723 1730 6.736794 GCACCTTGACAGAAGTTGAAATGAAT 60.737 38.462 0.00 0.00 0.00 2.57
1727 1734 3.953612 TGCACCTTGACAGAAGTTGAAAT 59.046 39.130 0.00 0.00 0.00 2.17
1754 1761 0.904865 CTCCAGTACCACCAGGCTCA 60.905 60.000 0.00 0.00 39.06 4.26
1820 1827 3.760035 GCTCGAGCTTCGGGGTGA 61.760 66.667 29.88 0.00 41.50 4.02
1853 1860 0.676151 GCTGGCTTGAGAAGTCCAGG 60.676 60.000 19.50 8.79 45.17 4.45
1955 1962 2.157738 CCCTCAGCTCTTCCACAAAAG 58.842 52.381 0.00 0.00 0.00 2.27
2000 2007 1.302511 TGCCTCTTCAAAGCCGGTC 60.303 57.895 1.90 0.00 0.00 4.79
2203 2210 8.440059 CAATCAAAACACAATCCAGATGATTTG 58.560 33.333 0.00 0.00 41.85 2.32
2212 2219 7.111247 AGAGAAACAATCAAAACACAATCCA 57.889 32.000 0.00 0.00 0.00 3.41
2250 2257 5.925506 TTGACGATGGGTATTCAGAGTTA 57.074 39.130 0.00 0.00 0.00 2.24
2356 2363 2.567049 CTCCGTCACCGACTCACC 59.433 66.667 0.00 0.00 35.63 4.02
2364 2371 0.460987 CCTGATCAAGCTCCGTCACC 60.461 60.000 0.00 0.00 0.00 4.02
2368 2375 3.356529 AAAATCCTGATCAAGCTCCGT 57.643 42.857 0.00 0.00 0.00 4.69
2833 2873 4.096732 AGCGAAAGAACATGCATAAACC 57.903 40.909 0.00 0.00 0.00 3.27
2897 2937 4.209538 ACACCTGGGTTTAAACAAGGTAC 58.790 43.478 29.94 11.43 42.31 3.34


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.